8WRY

Cryo-EM Structure of Mouse TLR4/MD-2/DLAM3 Complex

PDB DOI: https://doi.org/10.2210/pdb8WRY/pdb
EM Map EMD-37794: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2023-10-16 Released: 2024-10-23
Deposition Author(s): Fu, Y., Kim, H., Zamyatina, A., Kim, H.M.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structural insight on tailored modulation of TLR4-mediated pro-inflammatory response by disaccharide lipid A mimetics

Fu, Y., Kim, H.

To be published.

Macromolecule Content

Total Structure Weight: 179.72 kDa
Atom Count: 12,324
Modelled Residue Count: 1,462
Deposited Residue Count: 1,492
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphocyte antigen 96	A [auth C], B [auth D]	142	Mus musculus	Mutation(s): 0 Gene Names: Ly96
UniProt
Find proteins for Q9JHF9 (Mus musculus) Explore Q9JHF9 Go to UniProtKB: Q9JHF9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9JHF9
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth C] Focus chain B [auth D]	Go to GlyGen: Q9JHF9-1
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 4	C [auth B], D [auth A]	604	Mus musculus	Mutation(s): 0 Gene Names: Tlr4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QUK6 (Mus musculus) Explore Q9QUK6 Go to UniProtKB: Q9QUK6
IMPC: MGI:96824
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9QUK6
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain C [auth B] Focus chain D [auth A]	Go to GlyGen: Q9QUK6-1
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H, I E, F, G, H, I, J	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0IL (Subject of Investigation/LOI) Query on 0IL Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain Q [auth D] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D]	L [auth C], Q [auth D]	(3R)-3-(tetradecanoyloxy)tetradecanoic acid C₂₈ H₅₄ O₄ IYESSKQVAKTOQB-AREMUKBSSA-N		Interactions Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain L [auth C] Focus chain Q [auth D]
2IL (Subject of Investigation/LOI) Query on 2IL Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain R [auth D] MOL2 format, chain K [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth D] mmCIF format, chain K [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth D]	K [auth C], M [auth C], P [auth D], R [auth D]	(3R)-3-(dodecanoyloxy)tetradecanoic acid C₂₆ H₅₀ O₄ IKRFTYQBIVDIMM-XMMPIXPASA-N		Interactions Focus chain K [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth D] Interactions & Density Focus chain K [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth D]
GP4 (Subject of Investigation/LOI) Query on GP4 Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain U [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain U [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain U [auth B]	DA [auth A], U [auth B]	2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose C₆ H₁₄ N O₈ P QWDBGVNDGYUIAC-UKFBFLRUSA-N		Interactions Focus chain DA [auth A] Focus chain U [auth B] Interactions & Density Focus chain DA [auth A] Focus chain U [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] EA [auth A] FA [auth A] GA [auth A] AA [auth B], BA [auth B], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], N [auth C], O [auth C], S [auth D], T [auth D], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
XIQ (Subject of Investigation/LOI) Query on XIQ Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain V [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain V [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain V [auth B]	CA [auth A], V [auth B]	2-(hydroxymethyl)-5-methoxy-3,6-bis(oxidanyl)pyran-4-one C₇ H₈ O₆ GVIOTWHHRIHYQC-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain V [auth B] Interactions & Density Focus chain CA [auth A] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Korea, Republic Of	Institute for Basic Science, IBS

Revision History (Full details and data files)

Version 1.0: 2024-10-23
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection
Version 2.0: 2025-02-05
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary